Contacts of the helix formed by residues 13 - 25 (chain D) in PDB entry 2IHU
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with THR 13 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11D LYS 3.7 14.4 - - - +
12D PRO* 1.3 73.9 - - - +
14D ALA* 1.3 65.6 + - - +
15D ALA* 3.3 22.2 + - - +
16D HIS* 3.0 9.2 + - - +
17D ALA* 3.0 19.8 + - - +
40D SER 4.4 3.5 + - - +
45D GLU* 5.5 1.9 + - - +
173D LEU 3.6 7.2 + - - -
174D GLY* 3.5 22.2 - - - +
175D SER 3.3 16.8 - - - -
176D SER* 4.0 3.4 - - - +
179D ILE* 3.5 7.2 - - - +
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Residues in contact with ALA 14 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D THR* 1.3 72.6 - - - +
15D ALA* 1.3 51.6 + - - +
17D ALA* 3.7 5.0 - - - +
18D LEU* 2.8 35.7 + - - +
139D LEU* 4.5 6.3 - - + -
142D PRO* 3.8 22.4 - - + +
145D ILE* 3.9 7.0 - - + +
172D LEU 3.4 24.9 - - - +
173D LEU* 3.6 10.0 - - + +
175D SER 2.8 11.2 + - - +
179D ILE* 3.2 9.1 - - + +
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Residues in contact with ALA 15 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D THR* 3.0 12.5 - - - +
14D ALA* 1.3 73.8 - - - +
16D HIS* 1.3 64.7 + - - +
18D LEU* 3.5 3.0 + - - +
19D LEU* 3.1 32.2 + - - +
40D SER 3.5 21.3 - - - +
41D ILE* 3.8 25.5 - - + +
45D GLU* 4.3 7.2 - - - +
173D LEU* 3.0 20.8 + - + +
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Residues in contact with HIS 16 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D PRO* 3.9 14.4 - - + +
13D THR* 3.0 21.5 + - - +
15D ALA* 1.3 76.4 - - - +
17D ALA* 1.3 61.1 - - - +
19D LEU 3.4 0.9 + - - -
20D SER* 2.8 41.3 + - - -
45D GLU* 3.7 43.1 + - + +
46D VAL* 3.7 12.2 - - + +
181D THR* 3.8 31.0 + - + +
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Residues in contact with ALA 17 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D THR 3.0 12.4 + - - +
14D ALA* 3.7 5.8 - - - +
16D HIS* 1.3 81.2 - - - +
18D LEU* 1.3 57.6 + - - +
20D SER* 3.8 4.8 - - - -
21D ARG* 3.0 30.3 + - - +
143D HIS 5.9 0.7 - - - +
145D ILE* 3.6 23.1 - - + +
146D THR* 4.3 11.9 + - - +
179D ILE* 4.6 17.5 - - + -
181D THR* 5.7 2.2 - - + -
185D ASN* 5.1 1.9 + - - +
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Residues in contact with LEU 18 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D ALA 2.8 21.5 + - - +
15D ALA 3.6 4.5 - - - +
16D HIS 3.2 0.2 - - - -
17D ALA* 1.3 73.6 - - - +
19D LEU* 1.3 65.5 + - + +
21D ARG* 3.3 4.6 + - - +
22D LEU* 3.1 39.3 + - + +
41D ILE* 4.7 4.3 - - + -
78D TRP* 3.7 30.1 - - + -
105D LEU* 4.3 16.8 - - + -
145D ILE* 3.9 20.3 - - + +
149D VAL* 3.6 24.2 - - + -
168D LEU* 3.8 20.6 - - + -
173D LEU* 4.2 11.0 - - + -
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Residues in contact with LEU 19 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D ALA 3.1 17.7 + - - +
18D LEU* 1.3 81.9 - - + +
20D SER* 1.3 56.5 + - - +
22D LEU* 3.4 12.6 + - + +
23D ARG* 3.0 28.9 + - - +
30D VAL* 4.3 17.5 - - + -
41D ILE* 4.0 15.7 - - + -
43D PHE* 4.0 34.5 - - + -
45D GLU* 3.5 33.4 - - + +
46D VAL* 3.7 20.2 - - + +
49D ILE* 4.0 17.4 - - + +
78D TRP* 5.9 0.9 - - + -
105D LEU* 6.3 0.2 - - + -
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Residues in contact with SER 20 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D HIS* 2.8 30.5 + - - -
17D ALA* 3.8 6.5 - - - -
19D LEU* 1.3 77.4 - - - +
21D ARG* 1.3 56.2 + - - +
23D ARG* 3.4 17.2 + - - +
24D ASP* 3.0 30.6 + - - +
46D VAL* 3.6 17.8 - - - +
185D ASN* 3.6 15.5 + - - -
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Residues in contact with ARG 21 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330B ARG* 3.8 6.1 - - - +
17D ALA 3.0 18.7 + - - +
18D LEU 3.3 3.8 + - - +
20D SER* 1.3 73.4 - - - +
22D LEU* 1.3 65.2 + - - +
24D ASP* 2.9 32.1 + - - +
25D HIS* 3.2 30.8 + - - -
146D THR* 3.6 29.5 - - + +
149D VAL* 3.8 24.9 - - + -
150D ASP* 2.8 42.9 + - - +
185D ASN* 3.4 9.8 - - - +
186D PRO* 2.7 33.7 + - - +
187D PRO 3.2 15.2 + - - -
188D ALA* 3.8 10.4 - - - +
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Residues in contact with LEU 22 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D LEU* 3.1 25.1 + - + +
19D LEU* 3.8 17.0 - - + +
21D ARG* 1.3 74.2 - - - +
23D ARG* 1.3 57.9 + - - +
25D HIS* 3.0 18.9 + - + -
27D VAL* 3.1 33.2 + - + +
30D VAL* 4.4 15.0 - - + -
49D ILE* 3.8 8.5 - - + -
76D ALA* 4.3 15.3 - - + -
103D ILE* 4.2 28.0 - - + -
105D LEU* 3.8 24.9 - - + -
149D VAL* 4.1 21.3 - - + -
153D VAL* 5.9 0.7 - - + -
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Residues in contact with ARG 23 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D LEU 3.0 17.4 + - - +
20D SER* 3.6 20.5 + - - +
21D ARG 3.2 0.2 - - - -
22D LEU* 1.3 76.7 - - - +
24D ASP* 1.3 66.4 + - - +
26D GLY* 2.9 19.6 + - - -
27D VAL 3.6 18.5 + - - +
46D VAL* 3.5 19.1 - - + +
47D GLU* 3.2 35.4 + - - +
48D GLY* 4.7 11.2 - - - +
49D ILE* 4.3 3.1 - - + +
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Residues in contact with ASP 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20D SER* 3.0 22.2 + - - +
21D ARG* 2.9 41.9 + - - +
23D ARG* 1.3 85.0 + - - +
25D HIS* 1.3 56.9 + - - +
26D GLY 3.4 2.3 + - - -
185D ASN* 3.0 24.3 + - - +
188D ALA* 3.4 19.7 - - + +
190D THR* 4.3 1.2 + - - -
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Residues in contact with HIS 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21D ARG* 3.2 26.2 + - + +
22D LEU* 3.0 10.4 + - + +
24D ASP* 1.3 74.6 - - - +
26D GLY* 1.3 58.7 - - - +
27D VAL* 3.4 12.1 + - + +
73D ARG* 5.3 3.5 - - - +
74D PRO* 4.5 11.3 - - + +
149D VAL* 3.9 15.9 - - + -
150D ASP* 2.8 31.8 + - - -
153D VAL* 3.8 38.5 - - + +
188D ALA* 3.5 28.7 - - + +
190D THR* 2.8 37.5 + - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il